diff options
| -rw-r--r-- | doc/man/indexamajig.1 | 2 | ||||
| -rw-r--r-- | libcrystfel/src/integration.c | 18 | ||||
| -rw-r--r-- | libcrystfel/src/integration.h | 3 | ||||
| -rw-r--r-- | src/indexamajig.c | 4 |
4 files changed, 19 insertions, 8 deletions
diff --git a/doc/man/indexamajig.1 b/doc/man/indexamajig.1 index 25bc1cd6..cb24e916 100644 --- a/doc/man/indexamajig.1 +++ b/doc/man/indexamajig.1 @@ -330,7 +330,7 @@ Do not record integrated reflections in the stream. The resulting output won't .PD 0 .IP \fB--int-diag=\fIcondition\fR\fR .PD -Show detailed information about reflection integration when \fIcondition\fR is met. The \fIcondition\fR can be \fBall\fR, \fBnone\fR, a set of Miller indices separated by commas, \fBrandom\fR or \fBnegative\fR. \fBrandom\fR means to show information about a random 1% of the peaks. \fBnegative\fR means to show peaks with intensities which are negative my more than 3 sigma. The default is \fB--int-diag=none\fR. +Show detailed information about reflection integration when \fIcondition\fR is met. The \fIcondition\fR can be \fBall\fR, \fBnone\fR, a set of Miller indices separated by commas, \fBrandom\fR, \fBimplausible\fR or \fBnegative\fR. \fBrandom\fR means to show information about a random 1% of the peaks. \fBnegative\fR means to show peaks with intensities which are negative my more than 3 sigma. \fBimplausible\fR means to show peaks with intensities which are negative my more than 5 sigma. The default is \fB--int-diag=none\fR. .SH BUGS ReAx indexing is experimental. It works very nicely for some people, and crashes for others. In a future version, it will be improved and fully supported. diff --git a/libcrystfel/src/integration.c b/libcrystfel/src/integration.c index 3111d345..83cf8d0e 100644 --- a/libcrystfel/src/integration.c +++ b/libcrystfel/src/integration.c @@ -1299,6 +1299,13 @@ static int get_int_diag(struct intcontext *ic, Reflection *refl) return i < -3.0*sigi; } + if ( ic->int_diag == INTDIAG_IMPLAUSIBLE ) { + double i, sigi; + i = get_intensity(refl); + sigi = get_esd_intensity(refl); + return i < -5.0*sigi; + } + if ( ic->int_diag == INTDIAG_INDICES ) { signed int h, k, l; get_indices(refl, &h, &k, &l); @@ -1565,12 +1572,6 @@ static void integrate_rings_once(Reflection *refl, struct image *image, sigma = sqrt(sig2_poisson + bx->m*sig2_bg); - if ( intensity < -5.0*sigma ) { - delete_box(ic, bx); - ic->n_implausible++; - return; - } - /* Record intensity and set redundancy to 1 */ bx->intensity = intensity; set_intensity(refl, intensity); @@ -1587,6 +1588,11 @@ static void integrate_rings_once(Reflection *refl, struct image *image, set_detector_pos(refl, 0.0, pfs, pss); if ( get_int_diag(ic, refl) ) show_peak_box(ic, bx); + + if ( intensity < -5.0*sigma ) { + ic->n_implausible++; + set_redundancy(refl, 0); + } } diff --git a/libcrystfel/src/integration.h b/libcrystfel/src/integration.h index 38cb8163..ec674128 100644 --- a/libcrystfel/src/integration.h +++ b/libcrystfel/src/integration.h @@ -40,7 +40,8 @@ typedef enum { INTDIAG_RANDOM, INTDIAG_ALL, INTDIAG_INDICES, - INTDIAG_NEGATIVE + INTDIAG_NEGATIVE, + INTDIAG_IMPLAUSIBLE } IntDiag; diff --git a/src/indexamajig.c b/src/indexamajig.c index b769d303..7aeccd53 100644 --- a/src/indexamajig.c +++ b/src/indexamajig.c @@ -552,6 +552,10 @@ int main(int argc, char *argv[]) iargs.int_diag = INTDIAG_NEGATIVE; } + if ( strcmp(int_diag, "implausible") == 0 ) { + iargs.int_diag = INTDIAG_IMPLAUSIBLE; + } + r = sscanf(int_diag, "%i,%i,%i", &h, &k, &l); if ( r == 3 ) { iargs.int_diag = INTDIAG_INDICES; |